Just make sure when you run make in a command line you get that it is looking for a makefile

Change into the bootloaders/zero directory

If you try to make all here and you get

fatal error: sam.h: No such file or directory

Make sure you've installed the Arduino SAM and SAMD packages through the board manager

Try make all again for success!

Before distributing, make sure to change the VID/PID in the makefile:

then run make clean and makeall again to make fresh files

When you're done, you'll have two new files, samd21_sam_ba.hex and samd21_sam_ba.bin

Programming into an Arduino Zero w/EDBG

The easiest way to do this is just replace samd21_sam_ba.bin in C:\Users\ladyada\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.6.4\bootloaders\zero (or where-ever the current version of your Arduino SAMD package is with the compiled samd21_sam_ba.bin

Launch the IDE, select Arduino Zero (programming port) from the Tools->Board menu, and Atmel EDBG as the Tools->Programmer

Then select Burn Bootloader

It only takes a few seconds to burn in the bootloader:

Feather M0 or Others

For this, you'll need to use an Atmel Studio or adalink setup, since you're using a J-Link or stlink.

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